plink --file hapmap1
plink --file hapmap1 --make-bed --out hapmap1
plink --file hapmap1 --make-bed --mind 0.05 --out highgeno
plink --bfile hapmap1
plink --bfile hapmap1 --missing --out miss_stat
more miss_stat.lmiss
more miss_stat.imiss
plink --bfile hapmap1 --chr 1 --out res1 --missing
plink --bfile hapmap1 --chr 2 --out res2 --missing
plink --bfile hapmap1 --freq --out freq_stat
plink --bfile hapmap1 --freq --within pop.phe --out freq_stat
more freq_stat.frq.strat
plink --bfile hapmap1 --snp rs1891905 --freq --within pop.phe --out snp1_frq_stat
plink --bfile hapmap1 --assoc --out as1
sort --key=7 -nr as1.assoc | head
plink --bfile hapmap1 --assoc --adjust --out as2
more as2.assoc.adjusted
plink --bfile hapmap1 --pheno pop.phe --assoc --adjust --out as3
plink --bfile hapmap1 --model --snp rs2222162 --out mod1
plink --bfile hapmap1 --model --cell 0 --snp rs2222162 --out mod2
plink --bfile hapmap1 --cluster --mc 2 --ppc 0.05 --out str1
more str1.cluster1
plink --bfile hapmap1 --mh --within str1.cluster2 --adjust --out aac1
more aac1.cmh.adjusted
plink --bfile hapmap1 --cluster --cc --ppc 0.01 --out version2
plink --bfile hapmap1 --mh --within version2.cluster2 --adjust --out aac2
plink --bfile hapmap1 --cluster --K 2 --out version3
plink --bfile hapmap1 --mh --within pop.phe --adjust --out aac3
plink --bfile hapmap1 --cluster --matrix --out ibd_view
## PLINK v1.90b4.9 64-bit (13 Oct 2017) www.cog-genomics.org/plink/1.9/
## (C) 2005-2017 Shaun Purcell, Christopher Chang GNU General Public License v3
## Logging to plink.log.
## Options in effect:
## --file hapmap1
##
## 193230 MB RAM detected; reserving 96615 MB for main workspace.
## Scanning .ped file... 0%1%2%3%4%5%6%7%8%10%11%12%13%14%15%16%17%19%20%21%22%23%24%25%26%28%29%30%31%32%33%34%35%37%38%39%40%41%42%43%44%46%47%48%49%50%51%52%53%55%56%57%58%59%60%61%62%64%65%66%67%68%69%70%71%73%74%75%76%77%78%79%80%82%83%84%85%86%87%88%89%91%92%93%94%95%96%97%98%100%
.ped scan complete (for binary autoconversion).
## Performing single-pass .bed write (83534 variants, 89 people).
## 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%
--file: plink.bed + plink.bim + plink.fam written.
## PLINK v1.90b4.9 64-bit (13 Oct 2017) www.cog-genomics.org/plink/1.9/
## (C) 2005-2017 Shaun Purcell, Christopher Chang GNU General Public License v3
## Logging to hapmap1.log.
## Options in effect:
## --file hapmap1
## --make-bed
## --out hapmap1
##
## 193230 MB RAM detected; reserving 96615 MB for main workspace.
## Scanning .ped file... 0%1%2%3%4%5%6%7%8%10%11%12%13%14%15%16%17%19%20%21%22%23%24%25%26%28%29%30%31%32%33%34%35%37%38%39%40%41%42%43%44%46%47%48%49%50%51%52%53%55%56%57%58%59%60%61%62%64%65%66%67%68%69%70%71%73%74%75%76%77%78%79%80%82%83%84%85%86%87%88%89%91%92%93%94%95%96%97%98%100%
.ped scan complete (for binary autoconversion).
## Performing single-pass .bed write (83534 variants, 89 people).
## 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%
--file: hapmap1-temporary.bed + hapmap1-temporary.bim + hapmap1-temporary.fam
## written.
## 83534 variants loaded from .bim file.
## 89 people (89 males, 0 females) loaded from .fam.
## 89 phenotype values loaded from .fam.
## Using 1 thread (no multithreaded calculations invoked).
## Before main variant filters, 89 founders and 0 nonfounders present.
## Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
## Total genotyping rate is 0.99441.
## 83534 variants and 89 people pass filters and QC.
## Among remaining phenotypes, 44 are cases and 45 are controls.
## --make-bed to hapmap1.bed + hapmap1.bim + hapmap1.fam ... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
## PLINK v1.90b4.9 64-bit (13 Oct 2017) www.cog-genomics.org/plink/1.9/
## (C) 2005-2017 Shaun Purcell, Christopher Chang GNU General Public License v3
## Logging to highgeno.log.
## Options in effect:
## --file hapmap1
## --make-bed
## --mind 0.05
## --out highgeno
##
## 193230 MB RAM detected; reserving 96615 MB for main workspace.
## Scanning .ped file... 0%1%2%3%4%5%6%7%8%10%11%12%13%14%15%16%17%19%20%21%22%23%24%25%26%28%29%30%31%32%33%34%35%37%38%39%40%41%42%43%44%46%47%48%49%50%51%52%53%55%56%57%58%59%60%61%62%64%65%66%67%68%69%70%71%73%74%75%76%77%78%79%80%82%83%84%85%86%87%88%89%91%92%93%94%95%96%97%98%100%
.ped scan complete (for binary autoconversion).
## Performing single-pass .bed write (83534 variants, 89 people).
## 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%
--file: highgeno-temporary.bed + highgeno-temporary.bim +
## highgeno-temporary.fam written.
## 83534 variants loaded from .bim file.
## 89 people (89 males, 0 females) loaded from .fam.
## 89 phenotype values loaded from .fam.
## 0 people removed due to missing genotype data (--mind).
## Using 1 thread (no multithreaded calculations invoked).
## Before main variant filters, 89 founders and 0 nonfounders present.
## Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
## Total genotyping rate is 0.99441.
## 83534 variants and 89 people pass filters and QC.
## Among remaining phenotypes, 44 are cases and 45 are controls.
## --make-bed to highgeno.bed + highgeno.bim + highgeno.fam ... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
## PLINK v1.90b4.9 64-bit (13 Oct 2017) www.cog-genomics.org/plink/1.9/
## (C) 2005-2017 Shaun Purcell, Christopher Chang GNU General Public License v3
## Logging to plink.log.
## Options in effect:
## --bfile hapmap1
##
## Warning: No output requested. Exiting.
##
## plink [input flag(s)...] {command flag(s)...} {other flag(s)...}
## plink --help {flag name(s)...}
##
## Commands include --make-bed, --recode, --flip-scan, --merge-list,
## --write-snplist, --list-duplicate-vars, --freqx, --missing, --test-mishap,
## --hardy, --mendel, --ibc, --impute-sex, --indep-pairphase, --r2, --show-tags,
## --blocks, --distance, --genome, --homozyg, --make-rel, --make-grm-gz,
## --rel-cutoff, --cluster, --pca, --neighbour, --ibs-test, --regress-distance,
## --model, --bd, --gxe, --logistic, --dosage, --lasso, --test-missing,
## --make-perm-pheno, --tdt, --qfam, --annotate, --clump, --gene-report,
## --meta-analysis, --epistasis, --fast-epistasis, and --score.
##
## 'plink --help | more'